-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_19542407-19661999

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.23657_t
Valid prediction for snap_scaffold_5-snap.3700-T1
Couldn't classify 77344, 77555
Couldn't classify 79937, 80035
Sorry, prediction pasa_asmbl_44978.p1 fails validation.
(AGT)	 AC	77344-77555	GT	AGG
(CTG)	 AG	79018-79133	GT	AGG
(GCA)	 AG	79435-79562	GT	AGG
(GAT)	 AG	79937-80035	GT	AGG
add_exon() Sorry, pasa_asmbl_44978.p1 79018-79133-terminal-2 is invalid.
-recovered pasa_asmbl_44978.p1, terminal, 79018, 79133
-recovered pasa_asmbl_44978.p1, internal, 79018, 79133
-recovered pasa_asmbl_44978.p1, internal, 79435, 79562
-recovered pasa_asmbl_44978.p1, internal, 79937, 80035
Valid prediction for GlimmerHMM_glimmerT_14178-T1
Valid prediction for GlimmerHMM_glimmerT_14180-T1
Valid prediction for GlimmerHMM_glimmerT_14171-T1
Valid prediction for GlimmerHMM_glimmerT_14165-T1
Valid prediction for snap_scaffold_5-snap.3683-T1
Valid prediction for GlimmerHMM_glimmerT_14183-T1
Valid prediction for snap_scaffold_5-snap.3685-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14181-T1
Valid prediction for GeneMark_model.23661_t
Valid prediction for snap_scaffold_5-snap.3698-T1
Valid prediction for snap_scaffold_5-snap.3694-T1
Valid prediction for GlimmerHMM_glimmerT_14170-T1
Valid prediction for snap_scaffold_5-snap.3695-T1
Valid prediction for GeneMark_model.23660_t
Couldn't classify 59490, 59655
Couldn't classify 66172, 66260
Sorry, prediction pasa_asmbl_44976.p1 fails validation.
(GAG)	 AC	59490-59655	GT	CAG
(ATG)	 AG	60377-60492	GT	AGG
(GTT)	 AG	62492-62617	GT	AAG
(CAT)	 AG	65391-65526	GT	GGG
(GTT)	 AG	66172-66260	AG	CCA
add_exon() Sorry, pasa_asmbl_44976.p1 60377-60492-initial-1 is invalid.
-recovered pasa_asmbl_44976.p1, initial, 60377, 60492
-recovered pasa_asmbl_44976.p1, internal, 60377, 60492
-recovered pasa_asmbl_44976.p1, internal, 62492, 62617
-recovered pasa_asmbl_44976.p1, internal, 65391, 65526
Valid prediction for snap_scaffold_5-snap.3696-T1
Valid prediction for GeneMark_model.23651_t
Valid prediction for GeneMark_model.23665_t
Valid prediction for GlimmerHMM_glimmerT_14175-T1
Valid prediction for GlimmerHMM_glimmerT_14164-T1
Valid prediction for snap_scaffold_5-snap.3684-T1
Valid prediction for GlimmerHMM_glimmerT_14172-T1
Valid prediction for GlimmerHMM_glimmerT_14177-T1
Valid prediction for snap_scaffold_5-snap.3697-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GlimmerHMM_glimmerT_14169-T1
Valid prediction for GlimmerHMM_glimmerT_14176-T1
Valid prediction for GlimmerHMM_glimmerT_14182-T1
Valid prediction for GeneMark_model.23664_t
Valid prediction for GeneMark_model.23649_t
Valid prediction for GeneMark_model.23655_t
Couldn't classify 76422, 76454
Sorry, prediction pasa_asmbl_46296.p1 fails validation.
(ATT)	 CT	76422-76454	GT	AGG
(GTG)	 AG	76534-76601	GT	AGG
(GTG)	 AG	76722-77090	GT	AGG
(ATT)	 AG	78378-78630	TG	AGT
-recovered pasa_asmbl_46296.p1, terminal, 78378, 78630
-recovered pasa_asmbl_46296.p1, internal, 76534, 76601
-recovered pasa_asmbl_46296.p1, internal, 76722, 77090
Valid prediction for snap_scaffold_5-snap.3693-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.23652_t
Valid prediction for snap_scaffold_5-snap.3686-T1
Valid prediction for GlimmerHMM_glimmerT_14173-T1
Valid prediction for snap_scaffold_5-snap.3691-T1
Valid prediction for GlimmerHMM_glimmerT_14168-T1
Valid prediction for GlimmerHMM_glimmerT_14166-T1
Valid prediction for GeneMark_model.23662_t
Valid prediction for GlimmerHMM_glimmerT_14174-T1
Valid prediction for snap_scaffold_5-snap.3692-T1
Valid prediction for snap_scaffold_5-snap.3688-T1
Valid prediction for GlimmerHMM_glimmerT_14179-T1
Valid prediction for snap_scaffold_5-snap.3701-T1
Valid prediction for GeneMark_model.23653_t
Valid prediction for GlimmerHMM_glimmerT_14167-T1
Valid prediction for snap_scaffold_5-snap.3687-T1
Valid prediction for snap_scaffold_5-snap.3699-T1
Valid prediction for GeneMark_model.23663_t
Valid prediction for snap_scaffold_5-snap.3690-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.23659_t
Valid prediction for snap_scaffold_5-snap.3689-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 119593
-exon list size: 172


building trellis

0.6    
1.1    
1.7    
2.3    
2.9    
3.4    
4.0    
4.6    
5.2    
5.7    
6.3    
6.9    
7.5    
8.0    
8.6    
9.2    
9.8    
10.3    
10.9    
11.5    
12.1    
12.6    
13.2    
13.8    
14.4    
14.9    
15.5    
16.1    
16.7    
17.2    
17.8    
18.4    
19.0    
19.5    
20.1    
20.7    
21.3    
21.8    
22.4    
23.0    
23.6    
24.1    
24.7    
25.3    
25.9    
26.4    
27.0    
27.6    
28.2    
28.7    
29.3    
29.9    
30.5    
31.0    
31.6    
32.2    
32.8    
33.3    
33.9    
34.5    
35.1    
35.6    
36.2    
36.8    
37.4    
37.9    
38.5    
39.1    
39.7    
40.2    
40.8    
41.4    
42.0    
42.5    
43.1    
43.7    
44.3    
44.8    
45.4    
46.0    
46.6    
47.1    
47.7    
48.3    
48.9    
49.4    
50.0    
50.6    
51.1    
51.7    
52.3    
52.9    
53.4    
54.0    
54.6    
55.2    
55.7    
56.3    
56.9    
57.5    
58.0    
58.6    
59.2    
59.8    
60.3    
60.9    
61.5    
62.1    
62.6    
63.2    
63.8    
64.4    
64.9    
65.5    
66.1    
66.7    
67.2    
67.8    
68.4    
69.0    
69.5    
70.1    
70.7    
71.3    
71.8    
72.4    
73.0    
73.6    
74.1    
74.7    
75.3    
75.9    
76.4    
77.0    
77.6    
78.2    
78.7    
79.3    
79.9    
80.5    
81.0    
81.6    
82.2    
82.8    
83.3    
83.9    
84.5    
85.1    
85.6    
86.2    
86.8    
87.4    
87.9    
88.5    
89.1    
89.7    
90.2    
90.8    
91.4    
92.0    
92.5    
93.1    
93.7    
94.3    
94.8    
95.4    
96.0    
96.6    
97.1    
97.7    
98.3    
98.9    
99.4    
-found 19 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 108976 - 119593
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 109134 - 119593
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support